RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.jOWoGN/RM_3919376.TueSep90422352025
Search Engine = rmblast 2.14.1+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1757416955
Database = /dev/shm/rModeler.jOWoGN/GCA_004307905.1_Dicsqu464_1 
  - Sequences = 467
  - Bases = 39597219
  - N50 = 218703
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  2208858-2366563 |                                                   [ 1 ]
  2051154-2208858 |                                                   [  ]
  1893450-2051154 |                                                   [  ]
  1735746-1893450 |                                                   [  ]
  1578042-1735746 |                                                   [  ]
  1420338-1578042 |                                                   [ 1 ]
  1262634-1420338 |                                                   [  ]
  1104930-1262634 |                                                   [  ]
  947226-1104930  |                                                   [ 1 ]
  789522-947226   |                                                   [ 1 ]
  631818-789522   |                                                   [ 2 ]
  474114-631818   |                                                   [ 7 ]
  316410-474114   |*                                                  [ 11 ]
  158706-316410   |******                                             [ 48 ]
  1002-158706     |************************************************** [ 395 ]

Storage Throughput = excellent ( 1614.11 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39597175 bp ( 38592056 non ambiguous )
   - Num Contigs Represented = 467
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 250 raw families identified
   - RepeatScout: Running filtering stage.. 250 families remaining
   - RepeatScout: 00:00:57 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 248 families... 00:00:37 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 1 satellite(s), 57 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:39 (hh:mm:ss) Elapsed Time : 190 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2130 repeats masked totaling 812390 bp(s).
   - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10278805 bp
       Num Contigs Represented = 197
       Non ambiguous bp:
             Initial: 10017562 bp
             After Masking: 9197468 bp
             Masked: 8.19 % 
 -- Input Database Coverage: 10278805 bp out of 39597219 bp ( 25.96 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 55611
Comparison Time: 00:04:11 (hh:mm:ss) Elapsed Time, 3425 HSPs Collected
Number of families returned by RECON: 839
Round Time: 00:04:48 (hh:mm:ss) Elapsed Time : 3 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6119 repeats masked totaling 2361280 bp(s).
   - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29318341 bp
       Num Contigs Represented = 404
       Non ambiguous bp:
             Initial: 28574465 bp
             After Masking: 26193397 bp
             Masked: 8.33 % 
 -- Input Database Coverage: 39597146 bp out of 39597219 bp ( 100.00 % )
Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 453628
Comparison Time: 00:16:29 (hh:mm:ss) Elapsed Time, 25498 HSPs Collected
Number of families returned by RECON: 3907
Round Time: 00:17:39 (hh:mm:ss) Elapsed Time : 23 families discovered.

RepeatScout/RECON discovery complete: 216 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.jOWoGN/RM_3919376.TueSep90422352025
# Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib
#   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Classification Time: 00:00:27 (hh:mm:ss) Elapsed Time


Program Time: 00:24:33 (hh:mm:ss) Elapsed Time